2OOL

Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome RpBphP3 from R. palustris


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZTUmodified PDB entry 1ZTU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6293protein concentration of 12mg/ml in 100 mM tri-sodium citrate pH 5.6, 6% isopropanol (v/v), and 7% PEG 4000 (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3963.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.866α = 90
b = 151.866β = 90
c = 75.996γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-02-22MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152006-02-09MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C
2SYNCHROTRONAPS BEAMLINE 19-ID0.97APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,22.15099.30.07710.713.95900958049
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.12.1810011

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTmodified PDB entry 1ZTU2.249.755138843956359593.290.191570.188280.23102RANDOM47.92
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
2.381.192.38-3.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.836
r_dihedral_angle_4_deg18.399
r_dihedral_angle_3_deg16.567
r_dihedral_angle_1_deg6.508
r_scangle_it2.671
r_scbond_it1.965
r_angle_refined_deg1.579
r_mcangle_it1.235
r_mcbond_it1.075
r_angle_other_deg0.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.836
r_dihedral_angle_4_deg18.399
r_dihedral_angle_3_deg16.567
r_dihedral_angle_1_deg6.508
r_scangle_it2.671
r_scbond_it1.965
r_angle_refined_deg1.579
r_mcangle_it1.235
r_mcbond_it1.075
r_angle_other_deg0.982
r_symmetry_vdw_refined0.461
r_symmetry_vdw_other0.425
r_nbd_refined0.21
r_nbd_other0.202
r_mcbond_other0.186
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.154
r_chiral_restr0.096
r_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4731
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms86

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
14BMCdata collection
HKL-2000data reduction